Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

"Hydridic Hydrogen-Bond Donors" Are Not Hydrogen-Bond Donors

Herein, we dismiss a recent proposal by Civiš, Hobza, and co-workers to modify the IUPAC definition of hydrogen bonds in order to expand the scope from protonic Y-Hδ+ to hydridic Y-Hδ- hydrogen-bond donor fragments [J. Am. Chem. Soc. 2023, 145, 8550]. Based on accurate Kohn-Sham molecular orbital (KS-MO) analyses, we falsify the conclusion that interactions involving protonic and hydridic hydrogens are both hydrogen bonds; they are not. Instead, our quantitative KS-MO, energy decomposition, and Voronoi deformation density analyses reveal two fundamentally different bonding mechanisms for protonic Y-Hδ+ and hydridic Y-Hδ- fragments which go with charge transfer in opposite directions. On one hand, we confirm the IUPAC definition for regular hydrogen bonds in the case of protonic Y-Hδ+ fragments. On the other hand, complexes involving Y-Hδ- fragments are, in fact, acceptors in other well-known families of Lewis-acid/base interactions, such as halogen bonds, chalcogen bonds, and pnictogen bonds. These mechanisms lead to the same spectroscopic phenomenon in both the Y-Hδ+ and Y-Hδ- fragments, that is, the redshift in the Y-H stretching frequency, which is, thus, not an exclusive indicator for hydrogen bonding.

Chalcogen Noncovalent Interactions between Diazines and Sulfur Oxides in Supramolecular Circular Chains

The noncovalent chalcogen interaction between SO2/SO3 and diazines was studied through a dispersion-corrected DFT Kohn-Sham molecular orbital together with quantitative energy decomposition analyses. For this, supramolecular circular chains of up to 12 molecules were built with the aim of checking the capability of diazine molecules to detect SO2/SO3 compounds within the atmosphere. Trends in the interaction energies with the increasing number of molecules are mainly determined by the Pauli steric repulsion involved in these σ-hole/π-hole interactions. But more importantly, despite the assumed electrostatic nature of the involved interactions, the covalent component also plays a determinant role in its strength in the involved chalcogen bonds. Noticeably, π-hole interactions are supported by the charge transfer from diazines to SO2/SO3 molecules. Interaction energies in these supramolecular complexes are not only determined by the S···N bond lengths but attractive electrostatic and orbital interactions also determine the trends. These results should allow us to establish the fundamental characteristics of chalcogen bonding based on its strength and nature, which is of relevance for the capture of sulfur oxides.

Pnictogen bond-driven control of the molecular interaction between organophosphorus and acetylcholinesterase enzyme

This study addresses a comprehensive assessment of the interaction between chemical warfare agents (CWA) and acetylcholinesterase (AChE) systems, focus on the intriguing pnictogen-bond interaction (PnB). Utilizing the crystallographic data from the Protein Data Bank pertaining to the AChE-CWA complex involving Sarin (GB), Cyclosarin (GF), 2-[fluoro(methyl)phosphoryl]oxy-1,1-dimethylcyclopentane (GP) and venomous agent X (VX) agents, the CWA is systematically displaced by increments of 0.1 Å along the PO bond axis, extending its distance by 4 Å from the original position. The AIM analysis was carried out and consistently revealed the presence of a significant interaction along the PO bond. Investigating the intrinsic nature of the PnB, the NBO and the EDA analysis unearthed the contribution of orbital factors to the overall energy of the system. Strikingly, this observation challenges the conventional σ-hole explanation commonly associated with such interactions. This finding adds a layer of complexity to understanding of PnB, encouraging further exploration into the underlying mechanisms governing these intriguing chemical phenomena.

Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?

This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.

A Charge-Charge Flux-Dipole Flux Analysis of Simple Molecular Systems with Halogen Bonds

The presence of halogen bonds (R-X···B; R = substituent group, X = halogen, and B = Lewis base) provides quite amazing molecular systems for electronic structure investigations, presenting unique characteristics of fundamental relevance to supramolecular chemistry among other areas. Here, we use a double-hybrid approach from Density Functional Theory and triple-ζ basis sets augmented with diffuse functions (B2PLYP/def2-TZVPD) to deal with a large group of simple molecular systems containing halogen bonds (XBs), focusing on geometrical structures, binding energies, harmonic vibrational frequencies, and fundamental infrared intensities. Next, the electron densities and their variations on vibrations are carefully studied with the Quantum Theory of Atoms in Molecules (QTAIM) formalism and the charge-charge flux-dipole flux (CCFDF) model. We notice that the R-X stretching mode usually shows vibrational frequency decrements and infrared intensifications during the XB formation. Such features were also observed in hydrogen bonds, although the explanation for the band strengthening is different. Surprisingly, the most important contribution to these intensity increments due to complexation is now the interaction term between the charge flux and dipole flux (CF × DF). Thus, the use of atomic dipoles is mandatory to fully understand this phenomenon. In fact, the huge charge flux contributions to changes in dipole moment derivatives of R-X stretchings on halogen bonding are no longer accompanied by opposite variations of similar magnitudes in polarizations described by atomic dipole fluxes, which provided nearly unaltered values during the XB formation. Thus, the electronic charge flux direction change that takes place in complexes (from B to R) now reinforces dipole moment derivative terms from such atomic polarizations (mainly from the X atom). This intermolecular charge flux seems to be responsible for the unusual features noticed in the R-X stretching mode with the CCDDF/QTAIM model.

2D-Graph of intermolecular interactions predicts radical character of anion-π* type charge-transfer complexes

The molecular orbital (MO) theory is one of the most useful methods to describe the formation of a new chemical bond between two molecules. However, it is less often employed for modelling non-bonded intermolecular interactions because of the small charge-transfer contribution. Here we introduce two simple descriptors, the energy difference (EDA) of the HOMO of an electron donor and the LUMO of an acceptor against such HOMO-LUMO overlap integral (SDA), to show that the MO theory could give a unified charge-transfer picture of both bonding and non-bonding interactions for two molecules. It is found that similar types of interactions tend to be closer to each other in this 2D graph. Notably, in a transition region from strong bonding to single-electron transfer, the interacting molecular pairs appear to present a "hybrid" between chemical bonding and a radical pair, such as anion-π* interactions. It is concluded that the number of nodes in the HOMO and LUMO play a crucial role in determining the bonding character of the molecular pair.

The interplay between hydrogen and halogen bonding: substituent effects and their role in the hydrogen bond enhanced halogen bond

The hydrogen bond enhanced halogen bond (HBeXB) has recently been used to effectively improve anion binding, organocatalysis, and protein structure/function. In this study, we present the first systematic investigation of substituent effects in the HBeXB. NMR analysis confirmed intramolecular HBing between the amine and the electron-rich belt of the XB donor (N-H⋯I). Gas-phase density functional theory studies showed that the influence of HBing on the halogen atom is more sensitive to substitution on the HB donor ring (R1). The NMR studies revealed that the intramolecular HBing had a significant impact on receptor performance, resulting in a 50-fold improvement. Additionally, linear free energy relationship (LFER) analysis was employed for the first time to study the substituent effect in the HBeXB. The results showed that substituents on the XB donor ring (R2) had a competing effect where electron donating groups strengthened the HB and weakened the XB. Therefore, selecting an appropriate substituent on the adjacent HB donor ring (R1) could be an alternative and effective way to enhance an electron-rich XB donor. X-ray crystallographic analysis demonstrated that intramolecular HBing plays an important role in the receptor adopting the bidentate conformation. Taken together, the findings imply that modifying distal substituents that affect neighboring noncovalent interactions can have a similar impact to conventional para substitution substituent effects.

Fluorescent nano-sized aggregates of halogen bonded complexes formed using perfluoropropyl iodides: a systematic comparison between two isomeric halogen bond acceptors, aniline and 4-methyl pyridine

The halogen bonds (XB) formed by the two isomers 4-methyl pyridine (MePy) and aniline (ANL) with heptafluoro-1-propyl iodide (n-C₃F₇I) and heptafluoro-2-propyl iodide (iso-C₃F₇I) were investigated using vibrational (FT-IR and Raman) spectroscopy and quantum mechanical calculations. While these two isomers indicated a distinctive impact on the ring related vibrations, molecular electrostatic potential, frontier molecular orbitals, intermolecular electron density delocalisation and consequential charge transfer upon halogen bonding with n-C₃F₇I and iso-C₃F₇I, the dramatic intermolecular charge transfer (CT) occurring on the MePy involved XB systems demonstrated an ion-pair like aggregation. Such aggregation, after 72 h and longer after mixing, leads to an emission of fluorescence for both [MePy·C₃F₇I] systems. The resulting nano-sized aggregates were characterised using UV-Vis absorption and fluorescence spectroscopy along with scanning and transmittance electron microscopy (SEM and TEM), wherein, the XB complex with iso-C₃F₇I showed a faster and more severe aggregation due to a stronger CT than that with n-C₃F₇I. The present work is the first case of aggregation induced emission (AIE) due to aggregation of XB complexes formed by small neutral molecules.

Structure and Bonding of Halonium Compounds

The geometrical parameters and the bonding in [D···X···D]⁺ halonium compounds, where D is a Lewis base with N as the donor atom and X is Cl, Br, or I, have been investigated through a combined structural and computational study. Cambridge Structural Database (CSD) searches have revealed linear and symmetrical [D···X···D]⁺ frameworks with neutral donors. By means of density functional theory (DFT), molecular electrostatic potential (MEP), and energy decomposition analyses (EDA) calculations, we have studied the effect of various halogen atoms (X) on the [D···X···D]⁺ framework, the effect of different nitrogen-donor groups (D) attached to an iodonium cation (X = I), and the influence of the electron density alteration on the [D···I···D]⁺ halonium bond by variation of the R substituents at the N-donor upon the symmetry, strength, and nature of the interaction. The physical origin of the interaction arises from a subtle interplay between electrostatic and orbital contributions (σ-hole bond). Interaction energies as high as 45 kcal/mol suggest that halonium bonds can be exploited for the development of novel halonium transfer agents, in asymmetric halofunctionalization or as building blocks in supramolecular chemistry.

Exploring Au(i) involving halogen bonding with N-heterocyclic carbene Au(i) aryl complexes in crystalline media

Among the known types of non-covalent interactions with a Au(i) metal center, Au(i) involving halogen bonding (XB) remains a rare phenomenon that has not been studied systematically. Herein, using five N-heterocyclic carbene (NHC) Au(i) aryl complexes and two iodoperfluoroarenes as XB donors, we demonstrated that the XB involving the Au(i) metal center can be predictably obtained for neutral Au(i) complexes using the example of nine co-crystals. The presence of XB involving the Au(i) center was experimentally investigated by single-crystal X-ray diffraction and solid-state ¹³C CP-MAS NMR methods, and their nature was elucidated through DFT calculations, followed by electron density, electrostatic potential, and orbital analyses. The obtained results revealed a connection between the structure and HOMO localization of Au(i) complexes as XB acceptors, and the geometrical, electronic, and spectroscopic features of XB interactions, as well as the supramolecular structure of the co-crystals.

The Tetrel Bond and Tetrel Halide Perovskite Semiconductors

The ion pairs [Cs+•TtX3-] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX3, that are widely regarded as blockbuster materials for optoelectronic applications such as in solar cells. The 3D structures consist of an anionic inorganic tetrel halide framework stabilized by the cesium cations (Cs+). We use computational methods to show that the geometrical connectivity between the inorganic monoanions, [TtX3-]∞, that leads to the formation of the TtX64- octahedra and the 3D inorganic perovskite architecture is the result of the joint effect of polarization and coulombic forces driven by alkali and tetrel bonds. Depending on the nature and temperature phase of these perovskite systems, the Tt···X tetrel bonds are either indistinguishable or somehow distinguishable from Tt-X coordinate bonds. The calculation of the potential on the electrostatic surface of the Tt atom in molecular [Cs+•TtX3-] provides physical insight into why the negative anions [TtX3-] attract each other when in close proximity, leading to the formation of the CsTtX3 tetrel halide perovskites in the solid state. The inter-molecular (and inter-ionic) geometries, binding energies, and charge density-based topological properties of sixteen [Cs+•TtX3-] ion pairs, as well as some selected oligomers [Cs+•PbI3-]n (n = 2, 3, 4), are discussed.

Intermolecular Covalent Interactions: Nature and Directionality

Quantum chemical methods were employed to analyze the nature and the origin of the directionality of pnictogen (PnB), chalcogen (ChB), and halogen bonds (XB) in archetypal F_m Z⋅⋅⋅F^- complexes (Z=Pn, Ch, X), using relativistic density functional theory (DFT) at ZORA-M06/QZ4P. Quantitative Kohn-Sham MO and energy decomposition analyses (EDA) show that all these intermolecular interactions have in common that covalence, that is, HOMO-LUMO interactions, provide a crucial contribution to the bond energy, besides electrostatic attraction. Strikingly, all these bonds are directional (i.e., F-Z⋅⋅⋅F^- is approximately linear) despite, and not because of, the electrostatic interactions which, in fact, favor bending. This constitutes a breakdown of the σ-hole model. It was shown how the σ-hole model fails by neglecting both, the essential physics behind the electrostatic interaction and that behind the directionality of electron-rich intermolecular interactions. Our findings are general and extend to the neutral, weaker ClI⋅⋅⋅NH₃ , HClTe⋅⋅⋅NH₃ , and H₂ ClSb⋅⋅⋅NH₃ complexes.

Computationally rational design of metal-involving halogen bonds with π-covalency: Structures and bonding analysis

Traditional π-covalent interactions have been proved in the non-metal halogen bond adducts formed by chloride and halogenated triphenylamine-based radical cations. In this study, we have rationally designed two metal-involving halogen bond adducts with π-covalency property, such as [L1-Pd···I-PTZ]⁺ (i.e., 1) and [L2-Pd···I-PTZ]⁺ (i.e., 2), in which the square-planar palladium complexes serve as halogen bond acceptor and 3,7-diiodo-10H-phenothiazine radical cation (i.e., [I-PTZ]^•+ ) acts as halogen bond donor. Noncovalent interaction analysis and quantum theory of atoms in molecules analysis revealed that there are notable halogen bond interactions along the Pd···I direction without genuine chemical bond formed in both designed adducts. Energy decomposition analysis together with natural orbital for chemical valence calculations were performed to gain insight into their bonding nature, which demonstrated the presence of remarkable π-covalent interactions and σ-covalent interactions in both 1 and 2. We therefore proposed a new strategy for building the metal-involving halogen bonds with π-covalency property, which will help the further development of new types of halogen bonds.

Enhancing Effects of the Cyano Group on the C-X∙∙∙N Hydrogen or Halogen Bond in Complexes of X-Cyanomethanes with Trimethyl Amine: CH3−n(CN)nX∙∙∙NMe3, (n = 0–3; X = H, Cl, Br, I)

In this paper, density functional theory and wave function theory calculations are carried out to investigate the strength and nature of the intermolecular C-X∙∙∙N bond interaction as a function of the number of cyano groups, CN, in the X-bond donor while maintaining the X-bond acceptor as fixed. Specifically, complexes of X-cyanomethanes with trimethyl amine CH_3−n(CN)_nX∙∙∙NMe₃ (n = 0–3; X = H, Cl, Br, I) are used as model systems. Geometrical parameters and vibrational C-X-stretching frequencies as well as interaction energies are used as relevant indicators to gauge hydrogen or halogen bond strength in the complexes. Additional characteristics of interactions that link these complexes, i.e., hydrogen or halogen bonds, are calculated with the use of the following theoretical tools: the atoms in molecules (AIM) approach, the natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The results show that, for the specified X-center, the strength of C-X∙∙∙N interaction increases significantly and in a non-additive fashion with the number of CN groups. Moreover, the nature (noncovalent or partly covalent) of the interactions is revealed via the AIM approach.

Thermodynamics and Spectroscopy of Halogen- and Hydrogen-Bonded Complexes of Haloforms with Aromatic and Aliphatic Amines

Similarities and differences of halogen and hydrogen bonding were explored via UV–Vis and ¹H NMR measurements, X-ray crystallography and computational analysis of the associations of CHX₃ (X=I, Br, Cl) with aromatic (tetramethyl-p-phenylenediamine) and aliphatic (4-diazabicyclo[2,2,2]octane) amines. When the polarization of haloforms was taken into account, the strengths of these complexes followed the same correlation with the electrostatic potentials on the surfaces of the interacting atoms. However, their spectral properties were quite distinct. While the halogen-bonded complexes showed new intense absorption bands in the UV–Vis spectra, the absorptions of their hydrogen-bonded analogues were close to the superposition of the absorption of reactants. Additionally, halogen bonding led to a shift in the NMR signal of haloform protons to lower ppm values compared with the individual haloforms, whereas hydrogen bonding of CHX₃ with aliphatic amines resulted in a shift in the opposite direction. The effects of hydrogen bonding with aromatic amines on the NMR spectra of haloforms were ambivalent. Titration of all CHX₃ with these nucleophiles produced consistent shifts in their protons’ signals to lower ppm values, whereas calculations of these pairs produced multiple hydrogen-bonded minima with similar structures and energies, but opposite directions of the NMR signals’ shifts. Experimental and computational data were used for the evaluation of formation constants of some halogen- and hydrogen-bonded complexes between haloforms and amines co-existing in solutions.

The Importance of Electrostatics and Polarization for Noncovalent Interactions: Ionic Hydrogen Bonds vs Ionic Halogen Bonds

A series of 26 hydrogen-bonded complexes between Br- and halogen, oxygen and sulfur hydrogen-bond (HB) donors is investigated at the M06-2X/6-311 + G(2df,2p) level of theory. Analysis using a model in which Br- is replaced by a point charge shows that the interaction energy ([Formula: see text]) of the complexes is accurately reproduced by the scaled interaction energy with the point charge ([Formula: see text]).This is demonstrated by [Formula: see text] with a correlation coefficient, R2 =0.999. The only outlier is (Br-H-Br)-, which generally is classified as a strong charge-transfer complex with covalent character rather than a HB complex. [Formula: see text] can be divided rigorously into an electrostatic contribution ([Formula: see text]) and a polarization contribution ([Formula: see text]).Within the set of HB complexes investigated, the former varies between -7.2 and -32.7 kcal mol-1, whereas the latter varies between -1.6 and -11.5 kcal mol-1. Compared to our previous study of halogen-bonded (XB) complexes between Br- and C-Br XB donors, the electrostatic contribution is generally stronger and the polarization contribution is generally weaker in the HB complexes. However, for both types of bonding, the variation in interaction strength can be reproduced accurately without invoking a charge-transfer term. For the Br-···HF complex, the importance of charge penetration on the variation of the interaction energy with intermolecular distance is investigated. It is shown that the repulsive character of [Formula: see text] at short distances in this complex to a large extent can be attributed to charge penetration.

Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers

It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.

Non-covalent interactions atlas benchmark data sets 4: σ-hole interactions

The SH250×10 dataset presented here extends the Non-Covalent Interactions Atlas database (https://www.nciatlas.org) to complexes bound by σ-hole interactions - halogen, chalcogen and pnictogen bonds. It comprises 250 complexes where Cl, Br, I, S, Se, P and As interact with diverse electron donors. An accurate CCSD(T)/CBS benchmark is provided for ten points along a dissociation curve of each complex. The SH250×10 set is used in testing a wide variety of DFT functionals and semiempirical quantum-mechanical methods. In DFT calculations, the new data set exposes large errors of some functionals related to exaggerated charge transfer. The size and diversity of the data set have also been exploited in the reparametrization of a halogen-bond correction for the PM6 semiempirical method.

Characterization of Competing Halogen- and Hydrogen-Bonding Motifs in Simple Mixed Dimers of HCN and HX (X = F, Cl, Br, and I)

This work performs the first systematic comparison of hydrogen- and halogen-bonded configurations of the HCN/HX mixed dimer, where X = F, Cl, Br, and I. Eleven different minima have been characterized for these four heterogeneous dimers near the CCSD(T) complete basis set (CBS) limit. For each complex, two different hydrogen-bonded minima were identified: the global minimum where HX acts as the hydrogen bond donor and a local minimum where HX acts as the hydrogen bond acceptor. A halogen-bonded local minimum was also identified for all but the fluorine mixed dimer. To the best of our knowledge, three of the minima are identified here for the first time. The hydrogen- and halogen-bonded local minima of each complex become more energetically competitive with the global minimum as the atomic radius of the halogen atom increases. CCSD(T) relative energies of the hydrogen-bonded local minima computed near the CBS limit decrease from 4.5 kcal mol^-1 for HCN/HF to 2.9, 2.4, and 1.2 kcal mol^-1 for X = Cl, Br, and I, respectively. Corresponding relative energies for the halogen-bonded local minima range from 4.0 kcal mol^-1 for X = Cl to 2.7 kcal mol^-1 for X = Br and to as little as 0.5 kcal mol^-1 X = I. Harmonic vibrational frequency shifts reported here suggest that it may be feasible to differentiate between the various minima for X = Cl, Br, and I via spectroscopic analysis, as was the case for the HCN/HF dimer.

Rational Computational Design of Systems Exhibiting Strong Halogen Bonding Involving Fluorine in Bicyclic Diamine Derivatives

Perhaps the most controversial and rare aspect of the halogen bonding interaction is the potential of fluorine in compounds to serve as a halogen bond donor. In this note, we provide clear and convincing examples of hypothetical molecules in which fluorine is strongly halogen bonding in a metastable state. Of particular note is a polycyclic system inspired by Selectfluor, which has been controversially proposed to engage in halogen bonding.

From weak to strong interactions: structural and electron topology analysis of the continuum from the supramolecular chalcogen bonding to covalent bonds

The relationship between covalent and supramolecular bonding, and the criteria of the assignments of different interactions were explored via the review of selenium and tellurium containing structures in the Cambridge Structural Database and their computational analysis using Quantum Theory of Atoms in Molecules (QTAIM). This combined study revealed continuums of the interatomic Se⋯Br and Te⋯I distances, d_Ch⋯X, in the series of associations from the sums of the van der Waals radii of these atoms (r_Ch + r_X) to their covalent bond lengths. The electron densities, ρ(r), at Bond Critical Points (BCPs) along the chalcogen bond paths increased gradually from about 0.01 a.u. common for the non-covalent interactions to about 0.1 a.u. typical for the covalent bonds. The log ρ(r) values fell on the same linear trend line when plotted against normalized interatomic distances, R_XY = d_Ch⋯X/(r_Ch + r_X). The transition from the positive to negative values of the energy densities, H(r), at the BCPs (related to a changeover of essentially non-covalent into partially covalent interactions) were observed at R_XY ≈ 0.80. Synchronous changes of bonding characteristics with R_XY (similar to that found earlier in the halogen-bonded systems) designated normalized interatomic separation as a critical factor determining the nature of these bondings. The uninterrupted continuums of Te⋯I and Se⋯Br bond lengths and BCPs' characteristics signified an intrinsic link between limiting types of bonding involving chalcogen atoms and between covalent and supramolecular bonding in general.

Halogen bond promoted aryl migration of allylic alcohols under visible light irradiation

A simple and catalyst-free radical addition/1,2-aryl migration cascade process of ally alcohol driven by halogen bond was developed under visible light irradiation, featuring mild conditions, practical procedures, and broad substrate scope.

"Anti-electrostatic" Halogen Bonding between Ions of Like Charge

Halogen bonding occurs between molecules featuring Lewis acidic halogen substituents and Lewis bases. It is often rationalized as a predominantly electrostatic interaction and thus interactions between ions of like charge (e. g., of anionic halogen bond donors with halides) seem counter-intuitive. Herein, we provide an overview on such complexes. First, theoretical studies are described and their findings are compared. Next, experimental evidences are presented in the form of crystal structure database analyses, recent examples of strong "anti-electrostatic" halogen bonding in crystals, and the observation of such interactions also in solution. We then compare these complexes to select examples of "counter-intuitive" adducts formed by other interactions, like hydrogen bonding. Finally, we comment on key differences between charge-transfer and electrostatic polarization.

σ-Electrons Responsible for Cooperativity and Ring Equalization in Hydrogen-Bonded Supramolecular Polymers

We have quantum chemically analyzed the cooperative effects and structural deformations of hydrogen-bonded urea, deltamide, and squaramide linear chains using dispersion-corrected density functional theory at BLYP-D3(BJ)/TZ2P level of theory. Our purpose is twofold: (i) reveal the bonding mechanism of the studied systems that lead to their self-assembly in linear chains; and (ii) rationalize the C-C bond equalization in the ring moieties of deltamide and squaramide upon polymerization. Our energy decomposition and Kohn-Sham molecular orbital analyses reveal cooperativity in all studied systems, stemming from the charge separation within the σ-electronic system by charge transfer from the carbonyl oxygen lone pair donor orbital of one monomer towards the σ* N-H antibonding acceptor orbital of the neighboring monomer. This key orbital interaction causes the C=O bonds to elongate, which, in turn, results in the contraction of the adjacent C-C single bonds that, ultimately, makes the ring moieties of deltamide and squaramide to become more regular. Notably, the π-electron delocalization plays a much smaller role in the total interaction between the monomers in the chain.

Revisiting the covalent nature of halogen bonding: a polarized three-center four-electron bond

As an important intermolecular interaction, halogen bonding has been studied extensively, but its nature still suffers from controversy without one uniform essence. Electrostatics, charge transfer, polarization and dispersion are emphasized, but the covalent nature is usually overlooked except for the strong halogen bonding species I₃⁻, which is widely accepted as a result of a three-center four-electron (3c-4e) interaction. In our study, the potential energy surface of I₃⁻ has been evaluated to explore the dissociation from I₃⁻ to I₂⋯I⁻. We found that different from an equivalent 3c-4e bond in I₃⁻, I₂⋯I⁻ can be rationalized by a polarized one. In addition, when the orbitals are polarized, it is exactly what traditional charge transfer or the popular σ-hole picture describes. I₃⁻ can be described by the Lewis theory model with the middle I⁺ cation serving as the Lewis acid and two terminal I⁻ anions acting as Lewis base. Therefore, we further extended this model to a series of I-containing species with chemical composition of L–I⁺–L, F⁻–I⁺–L and H₃P–I⁺–L (L = OH⁻, F⁻, Cl⁻, Br⁻, I⁻, PH₃, NH₃, H₂S, HI, H₂O, HBr and HCl) to explore the nature of halogen bonding. When the forces of two bases around I⁺ are the same, it corresponds to an equivalent 3c-4e bond, such as I₃⁻. Otherwise, it is a polarized multicenter bond, such as I₂⋯I⁻. This work gives a new insight into the nature of halogen bonding compounds: besides the well-known I₃⁻, the nature of the other species is also a multicenter bond, existing as equivalent and polarized 3c-4e bonds, respectively.

The halogen bond could be described with a polarized 3c-4e bond.

Examining a Transition from Supramolecular Halogen Bonding to Covalent Bonds: Topological Analysis of Electron Densities and Energies in the Complexes of Bromosubstituted Electrophiles

The transition from weak (noncovalent) interactions to fully developed covalent bonds is examined using the quantum theory of atoms in molecules in a series of halogen-bonded (XB) complexes of bromosubstituted electrophiles, RBr, with 1,4-diazabicyclo[2.2.2]octane (DABCO) and Cl^- and Br^- anions. The gradual decrease in the XB lengths in these associations, d _Br···Y (where Y = Cl^-, Br^-, or N), was accompanied by the exponential increase in the binding energies and charge transfer, as well as electron densities and magnitudes of the kinetic and potential energy densities at the bond critical points (BCPs) on the Br···Y bond path. These indices, as well as characteristics of the adjacent bonds in the XB donor, followed remarkably close trend lines when plotted against the normalized XB length R _BrY = d _Br···Y/(r _Br + r _Y) (where r _Br and r _Y are the van der Waals radii) regardless of the methods [MP2/6-311+G(d,p) or M062X/6-311+G(d,p)], media (gas phase or dichloromethane), and nucleophiles (Cl^-, Br^-, or DABCO). In the systems with an R _BrY higher than about 0.78, the energy densities H(r) at BCPs at the Br···Y bond path were small and positive, and XBs did not substantially affect the characteristics of the adjacent R-Br covalent bond in the XB donor. Accordingly, the XB can be identified as noncovalent in this range. In the complexes with R _BrY values between about 0.67 and 0.78, energy densities H(r) at Br···Y BCPs were negative, and their magnitudes increased with the decrease in the Br···Y separation. In this range, formation of XBs was accompanied by the increase in the R-Br bond length in the XB donor and the decrease in the magnitude of the (negative) H(r) values at the BCPs of the R-Br bonds. XBs can be classified as partially covalent in this R _BrY range. At an R _BrY less than about 0.67, electron densities were larger, and energy densities were more negative at BCPs of the Br···Y bond than those at BCPs of the R-Br bond in the XB donor. This indicates that Br···Y bonds were stronger than R-Br bonds, and these (Br···Y) XBs can be regarded as essentially covalent. The synchronous change of a variety of (R-Br and Br···Y) bonding characteristics with R _BrY suggests that the normalized XB bond length can be used as a basic parameter in the identification of the type of intermolecular interaction. A continuity of these characteristics suggests an inherent relationship between limiting (covalent and noncovalent) types of XBs and thus an onset of molecular-orbital interactions in the weaker bonds.

Controlling the molecular arrangement of racemates through weak interactions: the synergy between π-interactions and halogen bonds

POX and NX halogen bonds in combination with π-stacking interactions lead to the sorting of π-extended R- and S-isomers. Theoretical calculations point to a positive synergistic effect between the π-interactions and the halogen bonds to be the origin of such phenomena. As a result, enantiomeric building blocks form homoleptically connected quadrangular structures.

The pnictogen bond: a quantitative molecular orbital picture

We have analyzed the structure and stability of archetypal pnictogen-bonded model complexes D3PnA- (Pn = N, P, As, Sb; D, A = F, Cl, Br) using state-of-the-art relativistic density functional calculations at the ZORA-M06/QZ4P level. We have accomplished two tasks: (i) to compute accurate trends in pnictogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. We have found that pnictogen bonds have a significant covalent character stemming from strong HOMO-LUMO interactions between the lone pair of A- and σ* of D3Pn. As such, the underlying mechanism of the pnictogen bond is similar to that of hydrogen, halogen, and chalcogen bonds.

Cooperative Self-Assembly in Linear Chains Based on Halogen Bonds

Cooperative properties of halogen bonds were investigated with computational experiments based on dispersion-corrected relativistic density functional theory. The bonding mechanism in linear chains of cyanogen halide (X-CN), halocyanoacetylene (X-CC-CN), and 4-halobenzonitrile (X-C6 H4 -CN) were examined for X = H, Cl, Br, and I. Our energy decomposition and Kohn-Sham molecular-orbital analyses revealed the bonding mechanism of the studied systems. Cyanogen halide and halocyanoacetylene chains possess an extra stabilizing effect with increasing chain size, whereas the 4-halobenzonitrile chains do not. This cooperativity can be traced back to charge separation within the σ-electronic system by charge-transfer between the lone-pair orbital of the nitrogen (σHOMO ) on one unit and the acceptor orbital of the C-X (σ*LUMO ) on the adjacent unit. As such, the HOMO-LUMO gap in the σ-system decreases, and the cooperativity increases with chain length revealing the similarity in the bonding mechanisms of hydrogen and halogen bonds.

"Anti-electrostatic" halogen bonding in solution

Halogen-bonded (XB) complexes between halide anions and a cyclopropenylium-based anionic XB donor were characterized in solution for the first time. Spontaneous formation of such complexes confirms that halogen bonding is sufficiently strong to overcome electrostatic repulsion between two anions. The formation constants of such "anti-electrostatic" associations are comparable to those formed by halides with neutral halogenated electrophiles. However, while the latter usually show charge-transfer absorption bands, the UV-Vis spectra of the anion-anion complexes examined herein are determined by the electronic excitations within the XB donor. The identification of XB anion-anion complexes substantially extends the range of the feasible XB systems, and it provides vital information for the discussion of the nature of this interaction.

Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

Chalcogen bonds: Hierarchical ab initio benchmark and density functional theory performance study

We have performed a hierarchical ab initio benchmark and DFT performance study of D2 Ch•••A- chalcogen bonds (Ch = S, Se; D, A = F, Cl). The ab initio benchmark study is based on a series of ZORA-relativistic quantum chemical methods [HF, MP2, CCSD, CCSD(T)], and all-electron relativistically contracted variants of Karlsruhe basis sets (ZORA-def2-SVP, ZORA-def2-TZVPP, ZORA-def2-QZVPP) with and without diffuse functions. The highest-level ZORA-CCSD(T)/ma-ZORA-def2-QZVPP counterpoise-corrected complexation energies (ΔECPC ) are converged within 1.1-3.4 kcal mol-1 and 1.5-3.1 kcal mol-1 with respect to the method and basis set, respectively. Next, we used the ZORA-CCSD(T)/ma-ZORA-def2-QZVPP (ΔECPC ) as reference data for analyzing the performance of 13 different ZORA-relativistic DFT approaches in combination with the Slater-type QZ4P basis set. We find that the three-best performing functionals are M06-2X, B3LYP, and M06, with mean absolute errors (MAE) of 4.1, 4.2, and 4.3 kcal mol-1 , respectively. The MAE for BLYP-D3(BJ) and PBE amount to 8.5 and 9.3 kcal mol-1 , respectively.

Role of Charge Transfer in Halogen Bonding

Halogen bonding has received intensive attention recently for its applications in the construction of supramolecular assemblies and crystal engineering and its implications and potentials in chemical and biological processes and rational drug design. Peculiarly, in intermolecular interactions, halogen atoms are known as electron-donating groups carrying partial negative charges in molecules due to its high electronegativity, but they can counterintuitively act as Lewis acids and bind with Lewis bases in the form of a halogen bond. The unsettling issue regarding the nature of the halogen bonding is whether the electrostatics or charge transfer interaction dominates. The recently proposed σ-hole concept nicely reinforces the role of electrostatic attraction. Also, good correlations between the halogen bonding strength and the interaction energy from the simple point-charge model have been found. This leads to the claim that there is no need to invoke the charge transfer concept in the halogen bond. But there is alternative evidence supporting the importance of charge transfer interaction. Here, we visited a series of prominent halogen bonded complexes of the types Y₃C-X···Z (X = Br, I; Y = F, Cl, Br; Z = F^-, Cl^-, Br^-, I^-, NMe₃) with the block-localized wave function (BLW) method at the M06-2X-D3/6-311+G(d,p) (def2-SVP for iodine) level of theory. As the simplest variant of ab initio valence bond (VB) theory, the BLW method is unique in the strict localization of electrons within interacting moieties, allowing for quantitative evaluation of the charge transfer effect on geometries, spectral properties, and energetics in halogen bonding complexes. By comparing the halogen bonding complexes with and without the charge transfer interaction, we proved that the charge transfer interaction significantly shortens the X···Z bonding distance and stretches the C-X bonds. But the shortening of the halogen bonding results in the less favorable steric effect, which is composed of Pauli repulsion, electrostatics, and electron correlation. There are approximate linear correlations between the charge transfer effect and binding energy and between bonding distance and binding energy. These correlations may lead to the illusion that the charge transfer interaction is unimportant or irrelevant, but further analyses showed that the inclusion of charge transfer is critical for the proper description of the halogen bonding, as considering only electrostatics and polarization leads to only about 45-60% of the binding strengths and much elongated bonding distances.

A Quantitative Molecular Orbital Perspective of the Chalcogen Bond

We have quantum chemically analyzed the structure and stability of archetypal chalcogen-bonded model complexes D2 Ch⋅⋅⋅A- (Ch = O, S, Se, Te; D, A = F, Cl, Br) using relativistic density functional theory at ZORA-M06/QZ4P. Our purpose is twofold: (i) to compute accurate trends in chalcogen-bond strength based on a set of consistent data; and (ii) to rationalize these trends in terms of detailed analyses of the bonding mechanism based on quantitative Kohn-Sham molecular orbital (KS-MO) theory in combination with a canonical energy decomposition analysis (EDA). At odds with the commonly accepted view of chalcogen bonding as a predominantly electrostatic phenomenon, we find that chalcogen bonds, just as hydrogen and halogen bonds, have a significant covalent character stemming from strong HOMO-LUMO interactions. Besides providing significantly to the bond strength, these orbital interactions are also manifested by the structural distortions they induce as well as the associated charge transfer from A- to D2 Ch.

Synthesis, Structure and Evaluation of the N-(2-Acetyl-4-(styryl)phenyl)-4-benzenesulfonamide Derivatives for Anticholinesterase and Antioxidant Activities

N-(2-Acetyl-4-bromophenyl)-4-methylbenzenesulfonamide (2) was transformed into 5-(4-methoxymethylstyryl)-2-(p-tolylsulfonamido)acetophenone (3a) and 5-(4- trifluoromethylstyryl)-2-(p-tolylsulfonamido)acetophenone (3b). Their structures were determined using a combination of NMR (1H & 13C) and mass spectroscopic as well as single crystal X-ray diffraction techniques. These compounds and the corresponding precursor, 2-amino-5-bromoacetophenone (1), were evaluated through enzymatic assays in vitro for inhibitory effect against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activities as well as antioxidant effect through the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and nitric oxide (NO) free radical scavenging assays. Molecular docking was performed on 3a to determine plausible protein–ligand interactions on a molecular level. Their drug likeness properties (absorption, distribution, metabolism, and excretion) and ability to cross the blood–brain barrier (BBB) have also been predicted at theoretical level.

Nature of the Hydrogen Bond Enhanced Halogen Bond

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.

Nature of Alkali- and Coinage-Metal Bonds versus Hydrogen Bonds

We have quantum chemically studied the structure and nature of alkali- and coinage-metal bonds (M-bonds) versus that of hydrogen bonds between A-M and B- in archetypal [A-M⋅⋅⋅B]- model systems (A, B=F, Cl and M=H, Li, Na, Cu, Ag, Au), using relativistic density functional theory at ZORA-BP86-D3/TZ2P. We find that coinage-metal bonds are stronger than alkali-metal bonds which are stronger than the corresponding hydrogen bonds. Our main purpose is to understand how and why the structure, stability and nature of such bonds are affected if the monovalent central atom H of hydrogen bonds is replaced by an isoelectronic alkali- or coinage-metal atom. To this end, we have analyzed the bonds between A-M and B- using the activation strain model, quantitative Kohn-Sham molecular orbital (MO) theory, energy decomposition analysis (EDA), and Voronoi deformation density (VDD) analysis of the charge distribution.

Lack of Cooperativity in the Triangular X3 Halogen-Bonded Synthon?

We have investigated 44 crystal structures, found in the Cambridge Structural Database, containing the X₃ synthon (where X = Cl, Br, I) in order to verify whether three type II halogen-halogen contacts forming the synthon exhibit cooperativity. A hypothesis that this triangular halogen-bonded motif is stabilized by cooperative effects is postulated on the basis of structural data. However, theoretical investigations of simplified model systems in which the X₃ motif is present demonstrate that weak synergy occurs only in the case of the I₃ motif. In the present paper we computationally investigate crystal structures in which the X₃ synthon is present, including halomesitylene structures, that are usually described as being additionally stabilized by a synergic interaction. Our computations find no cooperativity for halomesitylene trimers containing the X₃ motif. Only in the case of two other structures containing the I₃ synthon a very weak or weak synergy, i.e. the cooperative effect being stronger than -0.40 kcal mol^-1, is found. The crystal structure of iodoform has the most pronounced cooperativity of all investigated systems, amounting to about 10% of the total interaction energy.

The HOX⋯SO2 (X=F, Cl, Br, I) Binary Complexes: Implications for Atmospheric Chemistry

Sulfur dioxide and hypohalous acids (HOX, X=F, Cl, Br, I) are ubiquitous molecules in the atmosphere that are central to important processes like seasonal ozone depletion, acid rain, and cloud nucleation. We present the first theoretical examination of the HOX⋯SO₂ binary complexes and the associated trends due to halogen substitution. Reliable geometries were optimized at the CCSD(T)/aug-cc-pV(T+d)Z level of theory for HOF and HOCl complexes. The HOBr and HOI complexes were optimized at the CCSD(T)/aug-cc-pV(D+d)Z level of theory with the exception of the Br and I atoms which were modeled with an aug-cc-pwCVDZ-PP pseudopotential. 27 HOX⋯SO₂ complexes were characterized and the focal point method was employed to produce CCSDT(Q)/CBS interaction energies. Natural Bond Orbital analysis and Symmetry Adapted Perturbation Theory were used to classify the nature of each principle interaction. The interaction energies of all HOX⋯SO₂ complexes in this study ranged from 1.35 to 3.81 kcal mol^-1 . The single-interaction hydrogen bonded complexes spanned a range of 2.62 to 3.07 kcal mol^-1 , while the single-interaction halogen bonded complexes were far more sensitive to halogen substitution ranging from 1.35 to 3.06 kcal mol^-1 , indicating that the two types of interactions are extremely competitive for heavier halogens. Our results provide insight into the interactions between HOX and SO₂ which may guide further research of related systems.

Halogen Bonding in the Complexes of Brominated Electrophiles with Chloride Anions: From a Weak Supramolecular Interaction to a Covalent Br–Cl Bond

The wide-range variation of the strength of halogen bonds (XB) not only facilitates a variety of applications of this interaction, but it also allows examining the relation (and interconversion) between supramolecular and covalent bonding. Herein, the Br…Cl halogen bonding in a series of complexes of bromosubstituted electrophiles (R-Br) with chloride anions were examined via X-ray crystallographic and computational methods. Six co-crystals showing such bonding were prepared by evaporation of solutions of R-Br and tetra-n-propylammonium chloride or using Cl− anions released in the nucleophilic reaction of 1,4-diazabicyclo[2.2.2]octane with dichloromethane in the presence of R-Br. The co-crystal comprised networks formed by 3:3 or 2:2 halogen bonding between R-Br and Cl−, with the XB lengths varying from 3.0 Å to 3.25 Å. Analysis of the crystallographic database revealed examples of associations with substantially longer and shorter Br…Cl separations. DFT computations of an extended series of R–Br…Cl− complexes confirmed that the judicious choice of brominated electrophile allows varying halogen Br…Cl bond strength and length gradually from the values common for the weak intermolecular complexes to that approaching a fully developed covalent bond. This continuity of halogen bond strength in the experimental (solid-state) and calculated associations indicates a fundamental link between the covalent and supramolecular bonding.

On the reciprocal relationship between σ-hole bonding and (anti)aromaticity gain in ketocyclopolyenes

σ-Hole bonding interactions (e.g., tetrel, pnictogen, chalcogen, and halogen bonding) can polarize π-electrons to enhance cyclic [4n] π-electron delocalization (i.e., antiaromaticity gain) or cyclic [4n + 2] π-electron delocalization (i.e., aromaticity gain). Examples based on the ketocyclopolyenes: cyclopentadienone, tropone, and planar cyclononatetraenone are presented. Recognizing this relationship has implications, for example, for tuning the electronic properties of fulvene-based π-conjugated systems such as 9-fluorenone.

π covalency in the halogen bond

Halogen bonds are a highly directional class of intermolecular interactions widely employed in chemistry and chemical biology. This linear interaction is commonly viewed to be analogous to the hydrogen bond because hydrogen bonding models also intuitively describe the σ-symmetric component of halogen bonding. The possibility of π-covalency in a halogen bond is not contemplated in any known models. Here we present evidence of π-covalency being operative in halogen bonds formed between chloride and halogenated triphenylamine-based radical cations. We reach this conclusion through computational analysis of chlorine K-edge X-ray absorption spectra recorded on these halogen bonded pairs. In light of this result, we contend that halogen bonding is better described by analogy to metal coordination bonds rather than hydrogen bonds. Our revised description of the halogen bond suggests that these interactions could be employed to influence the electronic properties of conjugated molecules in unique ways.

An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Study of the Halogen Bond with Explicit Analysis of Electron Correlation

Energy profiles of seven halogen-bonded complexes were analysed with the topological energy partitioning called Interacting Quantum Atoms (IQA) at MP4(SDQ)/6-31+G(2d,2p) level of theory. Explicit interatomic electron correlation energies are included in the analysis. Four complexes combine X₂ (X = Cl or F) with HCN or NH₃, while the remaining three combine ClF with HCN, NH₃ or N₂. Each complex was systematically deformed by translating the constituent molecules along its central axis linking X and N, and reoptimising its remaining geometry. The Relative Energy Gradient (REG) method (Theor. Chem. Acc. 2017, 136, 86) then computes which IQA energies most correlate with the total energy during the process of complex formation and further compression beyond the respective equilibrium geometries. It turns out that the covalent energy (i.e., exchange) of the halogen bond, X…N, itself drives the complex formation. When the complexes are compressed from their equilibrium to shorter X…N distance then the intra-atomic energy of N is in charge. When the REG analysis is restricted to electron correlation then the interatomic correlation energy between X and N again drives the complex formation, and the complex compression is best described by the destabilisation of the through-space correlation energy between N and the "outer" halogen.

Cobaloximes as Building Blocks in Halogen-Bonded Cocrystals

In this work, we explore the halogen-bonded cocrystallization potential of cobaloxime complexes in the synthesis of cocrystals with perhalogenated benzenes. We demonstrate a strategy for synthesizing halogen-bonded metal–organic cocrystals by utilizing cobaloximes whose pendant bromide group and oxime oxygen enable halogen bonding. By combining three well-known halogen bond donor molecules differing in binding geometry and composition with three cobaloxime units, we obtained a total of four previously unreported cocrystals. Single crystal X-ray diffraction experiments showed that the majority of obtained cocrystals exhibited the formation of the targeted I···O and I···Br motives. These results illustrate the potential of cobaloximes as halogen bond acceptors and indicate that this type of halogen bond acceptors may offer a novel route to metal–organic halogen-bonded cocrystals.

Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins

Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish whether trimethylthialysine, a simple trimethyllysine analogue generated through cysteine alkylation, is a good trimethyllysine mimic for studies on molecular recognition by reader proteins. Histone peptides bearing trimethylthialysine and trimethyllysine were examined for binding with five human reader proteins employing a combination of thermodynamic analyses, molecular dynamics simulations and quantum chemical analyses. Collectively, our experimental and computational findings reveal that trimethylthialysine and trimethyllysine exhibit very similar binding characteristics for the association with human reader proteins, thereby justifying the use of trimethylthialysine for studies aimed at dissecting the origin of biomolecular recognition in epigenetic processes that play important roles in human health and disease.

Halogen Bonding Interactions of Polychlorinated Biphenyls and the Potential for Thyroid Disruption

Polychlorinated biphenyl (PCB) flame retardants are persistent pollutants and inhibit neurodevelopment, particularly in the early stages of life. Halogen bonding (XB) to the iodothyronine deiodinases (Dio) that modulate thyroid hormones (THs) is a potential mechanism for endocrine disruption. Cl⋅⋅⋅Se XB interactions of PCBs with SeMe- , a small model of the Dio active site selenocysteine, are compared with previous results on polybrominated diphenylethers (PBDEs) and THs using density functional theory. PCBs generally display weaker XB interactions compared to PBDEs and THs, consistent with the dependence of XB strength on the size of the halogen (I>Br>Cl). PCBs also do not meet a proposed energy threshold for substrates to undergo dehalogenation, suggesting they may behave as competitive inhibitors of Dio in addition to other mechanisms of endocrine disruption. XB interactions in PCBs are position-dependent, with ortho interactions slightly more favorable than meta and para interactions, suggesting that PCBs may have a greater effect on certain classes of Dio. Flexibility of PCBs around the biphenyl C-C bond is limited by ortho substitutions relative to the biphenyl linkage, which may contribute to the ability to inhibit Dio and other TH-related proteins.

A dual attack on the peroxide bond. The common principle of peroxidatic cysteine or selenocysteine residues

The (seleno)cysteine residues in some protein families react with hydroperoxides with rate constants far beyond those of fully dissociated low molecular weight thiol or selenol compounds. In case of the glutathione peroxidases, we could demonstrate that high rate constants are achieved by a proton transfer from the chalcogenol to a residue of the active site [Orian et al. Free Radic. Biol. Med. 87 (2015)]. We extended this study to three more protein families (OxyR, GAPDH and Prx). According to DFT calculations, a proton transfer from the active site chalcogenol to a residue within the active site is a prerequisite for both, creating a chalcogenolate that attacks one oxygen of the hydroperoxide substrate and combining the delocalized proton with the remaining OH or OR, respectively, to create an ideal leaving group. The “parking postions” of the delocalized proton differ between the protein families. It is the ring nitrogen of tryptophan in GPx, a histidine in GAPDH and OxyR and a threonine in Prx. The basic principle, however, is common to all four families of proteins. We, thus, conclude that the principle outlined in this investigation offers a convincing explanation for how a cysteine residue can become peroxidatic.

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In some protein families, (seleno)cysteine residues react with hydroperoxides with very high rate constants.

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In GPx, DFT models of the oxidation of the catalytic site support a two-step mechanism for the H₂O₂ reduction.

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This mechanism is here found to operate in other thiol-based enzymes, i.e. OxyR, GAPDH and Prx.